direct mapping between chormosomal positions between hg19 and hg38 dbSNP positions

Question

[jyoti.khadake]

Hi,

Is there a direct 1:1 mapping of positions between say dbSNP build 151 HG19 positions and HG38 positions available somewhere?

Thanks, Jyoti

[jyoti.khadake]

Thanks that works. This is where I got the originals anyway. best, J

[GenoMax]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

[jyoti.khadake]

PS. can I \T it so the output can be redirected?

[Pierre Lindenbaum]

just redirect the output like a standard cmd line, the formatting will be removed.

Answer 1

[Pierre Lindenbaum]

using mysql/ucsc:

$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306 -D hg38 -e 'select S1.name,S1.chrom,S1.chromStart,S1.chromEnd,S2.chrom,S2.chromStart,S2.chromEnd from hg19.snp150 as S1 , hg38.snp150 as S2 where S1.name=S2.name limit 20' 
+--------------+-------+------------+----------+-------+------------+----------+
| name         | chrom | chromStart | chromEnd | chrom | chromStart | chromEnd |
+--------------+-------+------------+----------+-------+------------+----------+
| rs775809821  | chr1  |      10019 |    10020 | chr1  |      10019 |    10020 |
| rs978760828  | chr1  |      10038 |    10039 | chr1  |      10038 |    10039 |
| rs1008829651 | chr1  |      10042 |    10043 | chr1  |      10042 |    10043 |
| rs1052373574 | chr1  |      10050 |    10051 | chr1  |      10050 |    10051 |
| rs892501864  | chr1  |      10054 |    10055 | chr1  |      10054 |    10055 |
| rs768019142  | chr1  |      10055 |    10055 | chr1  |      10055 |    10055 |
| rs1010989343 | chr1  |      10062 |    10063 | chr1  |      10062 |    10063 |
| rs1022805358 | chr1  |      10076 |    10077 | chr1  |      10076 |    10077 |
| rs62651026   | chr1  |      10107 |    10108 | chr1  |      10107 |    10108 |
| rs376007522  | chr1  |      10108 |    10109 | chr1  |      10108 |    10109 |
| rs796688738  | chr1  |      10128 |    10128 | chr1  |      10128 |    10128 |
| rs368469931  | chr1  |      10138 |    10139 | chr1  |      10138 |    10139 |
| rs144773400  | chr1  |      10144 |    10145 | chr1  |      10144 |    10145 |
| rs779258992  | chr1  |      10146 |    10147 | chr1  |      10146 |    10147 |
| rs371194064  | chr1  |      10149 |    10150 | chr1  |      10149 |    10150 |
| rs796884232  | chr1  |      10165 |    10165 | chr1  |      10165 |    10165 |
| rs201752861  | chr1  |      10176 |    10177 | chr1  |      10176 |    10177 |
| rs367896724  | chr1  |      10177 |    10177 | chr1  |      10177 |    10177 |
| rs201694901  | chr1  |      10179 |    10180 | chr1  |      10179 |    10180 |
| rs905327004  | chr1  |      10198 |    10199 | chr1  |      10198 |    10199 |
+--------------+-------+------------+----------+-------+------------+----------+

[ATpoint]

jyoti.khadake, don't be surprised that the coordinates in this case are the same between both genome versions. This is probably because these variants are at the very edge of chromosome 1 where no coordinate changes might have happened. If you go further down the list, e.g. setting limit to 10000 and tail would give you

rs867243565 chr1    667509  667510  chr1    732129  732130
rs1000204238    chr1    667550  667551  chr1    732170  732171
rs372806026 chr1    667626  667627  chr1    732246  732247
rs377315554 chr1    667630  667631  chr1    732250  732251
rs1053994779    chr1    667637  667638  chr1    732257  732258
rs369862000 chr1    667655  667656  chr1    732275  732276
rs201764515 chr1    667665  667666  chr1    732285  732286
rs893969505 chr1    667702  667703  chr1    732322  732323
rs879921095 chr1    667781  667782  chr1    732401  732402
rs1012409450    chr1    667813  667814  chr1    732433  732434

so coordinates are starting to changing at some point.